Dataset Information

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

ABSTRACT: Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

SUBMITTER: Dhar MS

PROVIDER: S-EPMC7612010 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

Dhar Mahesh S MS Marwal Robin R Vs Radhakrishnan R Ponnusamy Kalaiarasan K Jolly Bani B Bhoyar Rahul C RC Sardana Viren V Naushin Salwa S Rophina Mercy M Mellan Thomas A TA Mishra Swapnil S Whittaker Charles C Fatihi Saman S Datta Meena M Singh Priyanka P Sharma Uma U Ujjainiya Rajat R Bhatheja Nitin N Divakar Mohit Kumar MK Singh Manoj K MK Imran Mohamed M Senthivel Vigneshwar V Maurya Ranjeet R Jha Neha N Mehta Priyanka P A Vivekanand V Sharma Pooja P Vr Arvinden A Chaudhary Urmila U Soni Namita N Thukral Lipi L Flaxman Seth S Bhatt Samir S Pandey Rajesh R Dash Debasis D Faruq Mohammed M Lall Hemlata H Gogia Hema H Madan Preeti P Kulkarni Sanket S Chauhan Himanshu H Sengupta Shantanu S Kabra Sandhya S Gupta Ravindra K RK Singh Sujeet K SK Agrawal Anurag A Rakshit Partha P Nandicoori Vinay V Tallapaka Karthik Bharadwaj KB Sowpati Divya Tej DT Thangaraj K K Bashyam Murali Dharan MD Dalal Ashwin A Sivasubbu Sridhar S Scaria Vinod V Parida Ajay A Raghav Sunil K SK Prasad Punit P Sarin Apurva A Mayor Satyajit S Ramakrishnan Uma U Palakodeti Dasaradhi D Seshasayee Aswin Sai Narain ASN Bhat Manoj M Shouche Yogesh Y Pillai Ajay A Dikid Tanzin T Das Saumitra S Maitra Arindam A Chinnaswamy Sreedhar S Biswas Nidhan Kumar NK Desai Anita Sudhir AS Pattabiraman Chitra C Manjunatha M V MV Mani Reeta S RS Arunachal Udupi Gautam G Abraham Priya P Atul Potdar Varsha PV Cherian Sarah S SS

Science (New York, N.Y.) 20211014 6570

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated a ...[more]

PMID: 34648303

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Project description:With the progression of the global SARS-CoV-2 pandemic, the new variants have become more infectious and continue spreading at a higher rate than pre-existing ones. Thus, we conducted a study to explore the epidemiology of emerging variants of SARS-CoV-2 that circulated in Bangladesh from December 2020 to September 2021, representing the 2nd and 3rd waves. We collected new cases and deaths per million daily data with the reproduction rate. We retrieved 928 SARS-CoV-2 sequences from GISAID and performed phylogenetic tree construction and mutation analysis. Case counts were lower initially at the end of 2020, during January-February and April-May 2021, whereas the death toll reached the highest value of 1.587 per million on the first week of August and then started to decline. All the variants (α, β, δ, η) were prevalent in the capital city, Dhaka, with dispersion to large cities, such as Sylhet and Chattogram. The B.1.1.25 lineage was prevalent during December 2020, but the B.1.617.2/δ variant was later followed by the B.1.351/β variant. The phylogeny revealed that the various strains found in Bangladesh could be from numerous countries. The intra-cluster and inter-cluster communication began in Bangladesh soon after the virus arrived. The prominent amino acid substitution was D614G from December 2020 to July 2021 (93.5 to 100%). From February-April, one of the VOC's important mutations, N501Y substitution, was also estimated at 51.8%, 76.1%, and 65.1% for the α, β and γ variants, respectively. The γ variant's unique mutation K417T was detected only at 1.8% in February. Another frequent mutation was P681R, a salient feature of the δ variant, detected in June (88.2%) and July (100%). Furthermore, only one γ variant was detected during the entire second and third wave, whereas no η variant was observed in this period. This rapid growth in the number of variants identified across Bangladesh shows virus adaptation and a lack of strict quarantine, prompting periodic genomic surveillance to foresee the spread of new variants, if any, and to take preventive measures as soon as possible.

Project description:Since its advent, the pandemic has caused havoc in multiple waves due partly to amplified transmissibility and immune escape to vaccines. Delhi, India also witnessed brutal multiple peaks causing exponential rise in cases. Here we had retrospectively investigated clade variation, emergence of new lineages and varied clinical characteristics during those three peaks in order to understand the trajectory of the ongoing pandemic. In this study, a total of 123,378 samples were collected for a time span of 14 months (1 June 2020 to 3 August 2021) encompassing three different peaks in Delhi. A subset of 747 samples was processed for sequencing. Complete clinical and demographic details of all the enrolled cases were also collected. We detected 26 lineages across three peaks nonuniformly from 612 quality passed samples. The first peak was driven by diverse early variants, while the second one by B.1.36 and B.1.617.2, unlike third peak caused entirely by B.1.617.2. A total of 18,316 mutations with median of 34 were reported. Majority of mutations were present in less than 1% of samples. Differences in clinical characteristics across three peaks was also reported. To be ahead of the frequently changing course of the ongoing pandemic, it is of utmost importance that novel lineages be tracked continuously. Prioritized sequencing of sudden local outburst and community hot spots must be done to swiftly detect a novel mutation/lineage of potential clinical importance. IMPORTANCE Genome surveillance of the Delhi data provides a more detailed picture of diverse circulating lineages. The added value that the current study provides by clinical details of the patients is of importance. We looked at the shifting patterns of lineages, clinical characteristics and mutation types and mutation load during each successive infection surge in Delhi. The importance of widespread genomic surveillance cannot be stressed enough to timely detect new variants so that appropriate policies can be immediately implemented upon to help control the infection spread. The entire idea of genomic surveillance is to arm us with the clues as to how the novel mutations and/or variants can prove to be more transmissible and/or fatal. In India, the densely populated cities have an added concern of the huge burden that even the milder variants of the virus combined with co-morbidity can have on the community/primary health care centers.

Dataset Information

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

Publications

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

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